8JEI

Cryo-EM Structure of the compuond 5c-HCAR3-Gi complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structural basis for ligand recognition of the human hydroxycarboxylic acid receptor HCAR3.

Ye, F.Pan, X.Zhang, Z.Xiang, X.Li, X.Zhang, B.Ning, P.Liu, A.Wang, Q.Gong, K.Li, J.Zhu, L.Qian, C.Chen, G.Du, Y.

(2024) Cell Rep 43: 114895-114895

  • DOI: https://doi.org/10.1016/j.celrep.2024.114895
  • Primary Citation of Related Structures:  
    8JEI

  • PubMed Abstract: 

    Hydroxycarboxylic acid receptor 3 (HCAR3), a class A G-protein-coupled receptor, is an important cellular energy metabolism sensor with a key role in the regulation of lipolysis in humans. HCAR3 is deeply involved in many physiological processes and serves as a valuable target for the treatment of metabolic diseases, tumors, and immune diseases. Here, we report four cryoelectron microscopy (cryo-EM) structures of human HCAR3-Gi1 complexes with or without agonists: the endogenous ligand 3-hydroxyoctanoic acid, the drug niacin, the highly subtype-specific agonist compound 5c (4-(n-propyl)amino-3-nitrobenzoic acid), and the apo form. Together with mutagenesis and functional analyses, we revealed the recognition mechanisms of HCAR3 for different agonists. In addition, the key residues that determine the ligand selectivity between HCAR2 and HCAR3 were also illuminated. Overall, these findings provide a structural basis for the ligand recognition, activation, and selectivity and G-protein coupling mechanisms of HCAR3, which contribute to the design of HCAR3-targeting drugs with high efficacy and selectivity.


  • Organizational Affiliation

    Kobilka Institute of Innovative Drug Discovery, School of Medicine, the Chinese University of Hong Kong, Shenzhen 518172, Guangdong, China; Guangxi Key Laboratory of Special Biomedicine, School of Medicine, Guangxi University, Nanning 530004, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(i) subunit alpha-1A [auth C]351Homo sapiensMutation(s): 0 
Gene Names: GNAI1
EC: 3.6.5
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Find proteins for P63096 (Homo sapiens)
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PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupP63096
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1337Homo sapiensMutation(s): 0 
Gene Names: GNB1
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Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2C [auth G]56Homo sapiensMutation(s): 0 
Gene Names: GNG2
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GTEx:  ENSG00000186469 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
scFv16D [auth S]247Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Hydroxycarboxylic acid receptor 3E [auth A]387Homo sapiensMutation(s): 0 
Gene Names: HCAR3GPR109BHCA3HM74BNIACR2
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Find proteins for P49019 (Homo sapiens)
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PHAROS:  P49019
GTEx:  ENSG00000255398 
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UniProt GroupP49019
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Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CW3
Query on CW3

Download Ideal Coordinates CCD File 
F [auth A]3-nitro-4-(propylamino)benzoic acid
C10 H12 N2 O4
OVDGUTHABMXVMI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release